28 Result(s)

Article

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention

Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in ge...

Fabian Hausmann, Stefan Kurtz in Algorithms for Molecular Biology (2021)

Article

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits

To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing the ecosystem irreversibly, we sampled SMS analogous habitats from the Kairei and ...

Yuchen Han, Giorgio Gonnella, Nicole Adam, Axel Schippers… in Scientific Reports (2018)

Article

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research

A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obta...

Malte Mader, Ronald Simon, Stefan Kurtz in Journal of Clinical Bioinformatics (2014)

Article

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structu...

Fernando Meyer, Stefan Kurtz, Michael Beckstette in BMC Bioinformatics (2013)

Article

LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons

Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identifica...

Sascha Steinbiss, Sascha Kastens, Stefan Kurtz in Mobile DNA (2012)

Article

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction ...

Giorgio Gonnella, Stefan Kurtz in BMC Bioinformatics (2012)

Article

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarr...

Malte Mader, Ronald Simon, Sascha Steinbiss… in Journal of Clinical Bioinformatics (2011)

Article

Structator: fast index-based search for RNA sequence-structure patterns

The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence...

Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will… in BMC Bioinformatics (2011)

Article

Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8

The Mongolian gerbils are a good model to mimic the Helicobacter pylori-associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and comp...

Max Farnbacher, Thomas Jahns, Dirk Willrodt, Rolf Daniel, Rainer Haas… in BMC Genomics (2010)

Article

Selective regain of egfr gene copies in CD44⁺/CD24^-/lowbreast cancer cellular model MDA-MB-468

Increased transcription of oncogenes like the epidermal growth factor receptor (EGFR) is frequently caused by amplification of the whole gene or at least of regulatory sequences. Aim of this study was to pinpo...

Konstantin Agelopoulos, Burkhard Greve, Hartmut Schmidt, Heike Pospisil… in BMC Cancer (2010)

Article

CoCoNUT: an efficient system for the comparison and analysis of genomes

Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and so...

Mohamed I Abouelhoda, Stefan Kurtz, Enno Ohlebusch in BMC Bioinformatics (2008)

Article

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

The challenges of accurate gene prediction and enumeration are further aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet TEs play a substantial role in genome evolutio...

Stefan Kurtz, Apurva Narechania, Joshua C Stein, Doreen Ware in BMC Genomics (2008)

Article

Efficient computation of absent words in genomic sequences

Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are ma...

Julia Herold, Stefan Kurtz, Robert Giegerich in BMC Bioinformatics (2008)

Article

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic g...

David Ellinghaus, Stefan Kurtz, Ute Willhoeft in BMC Bioinformatics (2008)

Article

Optimising oligonucleotide array design for ChIP-on-chip

Fiona Nielsen, Stefan Graef, **nmin Zhang, Stefan Kurtz… in BMC Bioinformatics (2007)

Article

Fast index based algorithms and software for matching position specific scoring matrices

In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes ...

Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz in BMC Bioinformatics (2006)